<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
<head>
   <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
   <meta name="GENERATOR" content="Mozilla/4.72 [en] (X11; U; Linux 2.2.14-6.1.1smp i686) [Netscape]">
   <title>Completeness of distance restraints; output</title>
<link HREF="mailto:jurgenfd@gmail.com" REV="MADE">
</head>
<body bgcolor="#FFFFFF">

<h1>
Aqua program module</h1>

<h2>
Completeness of distance restraints</h2>

<h3>
Output</h3>

<hr>
<p>The completeness check and its application to a large set of structures
is described in:
<ul>
<li>
J.F. Doreleijers, M.L. Raves, J.A.C. Rullmann &amp; R. Kaptein. "Completeness
of NOEs in proteins: a statistical analysis of NMR data"
<i>J. Biomol.
NMR</i> (1999) <b>14</b>, 123-132.</li>
</ul>

<hr>
<h3>
Overview</h3>
The script <a href="complchk.html">complchk</a> produces the following
output in files:
<p><b>General data</b>
<table BORDER CELLPADDING=10 NOSAVE >
<tr NOSAVE>
<td></td>

<td NOSAVE>Filename&nbsp;</td>

<td>Description&nbsp;</td>
</tr>

<tr NOSAVE>
<td>1&nbsp;</td>

<td NOSAVE>PROJECT_comp_str.comp&nbsp;</td>

<td NOSAVE>All data in formatted tables. PROJECT is the name of the project.&nbsp;</td>
</tr>
</table>

<p><b>Sets of contacts</b>
<table BORDER CELLPADDING=10 NOSAVE >
<tr NOSAVE>
<td>2&nbsp;</td>

<td>exp.noe&nbsp;</td>

<td NOSAVE>Set A; All observable NOEs considered&nbsp;</td>
</tr>

<tr NOSAVE>
<td>3&nbsp;</td>

<td NOSAVE>model.noe&nbsp;</td>

<td>Set B; All observable model contacts considered&nbsp;</td>
</tr>

<tr>
<td>4&nbsp;</td>

<td>exp_nomatch.noe&nbsp;</td>

<td>Set A minus the intersection of set A and B&nbsp;</td>
</tr>

<tr>
<td>5&nbsp;</td>

<td>model_nomatch.noe&nbsp;</td>

<td>Set B minus the intersection of set A and B&nbsp;</td>
</tr>
</table>

<p><b>Log files</b>
<table BORDER CELLPADDING=10 NOSAVE >
<tr NOSAVE>
<td>6&nbsp;</td>

<td NOSAVE>complchk.log&nbsp;</td>

<td>completeness check&nbsp;</td>
</tr>

<tr>
<td>7&nbsp;</td>

<td>aqpc.log&nbsp;</td>

<td>aqpc (preparative step)&nbsp;</td>
</tr>
</table>

<p>
<hr>
<p>A description per file follows:
<br><b>General data</b>
<p><b>1</b> PROJECT_comp_str.comp
<br>The following blocks of data are present:
<ol>
<li>
GENERAL</li>

<li>
PARAMETERS</li>

<li>
SUMMARY_OVERALL</li>

<li>
COMPLETENESS_PER_SHELL</li>

<li>
COMPLETENESS_PER_CLASS</li>

<li>
COMPLETENESS_PER_ATOM_TYPE</li>

<li>
COMPLETENESS_PER_ATOM_TYPE</li>

<li>
COMPLETENESS_PER_RESIDUE_TYPE</li>

<li>
COMPLETENESS_PER_RESIDUE</li>

<li>
COMPLETENESS_PER_RESATOM</li>

<li>
COMPLETENESS_PER_ATOM <i>Only when option detail is true</i></li>

<li>
COMPLETENESS_AVERAGES_AND_SDS</li>

<li>
SSA_PER_TYPE <i>Only when option anal_ssa is true</i></li>

<li>
SSA_PER_ATOM <i>Only when options detail AND anal_ssa are true</i></li>
</ol>
The blocks can be extracted from the file, using dbext (see 'qhelp <a href="../doc/qdbext.txt">qdbext</a>').
Please read the EXPLAIN block in the file for a key to the abbreviations
used. If a number has been assigned to <b>-99.9</b> then this means the
number has no meaningful value.
<p>An example block, the COMPLETENESS_PER_RESIDUE is shown below:
<pre>$ DATA&nbsp; COMPLETENESS_PER_RESIDUE
$ TABLE #RECORDS 99 #ITEMS 10
Chn Resnm Res&nbsp; N_O_a&nbsp;&nbsp;&nbsp; N_P&nbsp;&nbsp; N_RM&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; C&nbsp; N_RnM&nbsp; N_sd Remark
_A GLU&nbsp;&nbsp;&nbsp; 17&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 36&nbsp;&nbsp;&nbsp;&nbsp; 13&nbsp;&nbsp; 36.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp; 0.9 _
.
.
_B LEU&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp; 75&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp; 6.7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp; -1.5 >sigma
$ END</pre>
The ten items (columns) are:
<ul>
<li>
<b>Chn</b> Chain identifier ("_" if none defined)</li>

<li>
<b>Resnm</b> Residue name</li>

<li>
<b>Res</b> Residue number</li>

<li>
<b>N_O_a</b> Number of Observable atoms for this residue</li>

<li>
<b>N_P</b> Number of Pairs (observable model contacts considered)</li>

<li>
<b>N_RM</b> Number of Restraints (NOEs considered) Matched to the observable
model contacts considered</li>

<li>
<b>C</b> Completeness for this residue</li>

<li>
<b>N_RnM</b> Number of Restraints (NOEs considered) that do not match the
observable model contacts considered.</li>

<li>
<b>N_sd</b> Number of standard deviations (sigmas) of the completeness
of this residue. The average value and standard deviation of completeness
over all residues are listed in the block called COMPLETENESS_AVERAGES_AND_SDS.</li>

<li>
<b>Remark</b> A remark, in this block the only remark can be ">sigma",
which means that the completeness of this residue is more than one sigma
below the average value of completeness over all residues.</li>
</ul>
<b>Sets of contacts</b>
<p><b>2</b> exp.noe
<br>A NOE restraint file in AQUA format using IUPAC recommended atom nomenclature
(<a href="http://www.bmrb.wisc.edu/home/iupac.pdf">Markley et al., 1998,
Pure &amp; Appl. Chem. 70, 117-142</a>). The restraints represent set A;
All observable NOEs considered. The type of NOE contact (<i>e.g.</i> NOEUPLO)
is the same as the input.
<p><b>3</b> model.noe
<br>A NOE restraint file in AQUA format using IUPAC recommended atom nomenclature.
The restraints represent set B; All observable model contacts considered.
The upper limit represents the maximum distance in the ensemble of structures
for this contact. The lower limit represents the minimum distance and the
target distance represents the average distance.
<p><b>4</b> exp_nomatch.noe
<br>Same as exp.noe but without the matched contacts; set A minus the intersection
of set A and B.
<p><b>5</b> model_nomatch.noe
<br>Same as model.noe but without the matched contacts; set B minus the
intersection of set A and B.<b></b>
<p><b>Log files</b>
<p><b>6</b> complchk.log
<br>The log file of the completeness check script (complchk) contains details
of all the results of the individual steps the script performs (see <a href="compl_method.html">method</a>).
The level of detail can be adjusted by the detail and terseness options
(see <a href="complchk.html">complchk</a>).
<p><b>7</b> aqpc.log
<br>The aqpc script first runs some preparative steps. You should at least
check that the number of NOEs you have provided is the same as the number
of NOEs that could be interpreted by AQUA as these are the only NOEs that
will be considered in the completeness check. More information about aqpc
and the output it produces can be found by typing 'qhelp <a href="../doc/aqpc.txt">aqpc</a>'.
<br>
<hr>
<p><b>NOTES</b>
<ul>
<li>
The script '<a href="complchk.html">complchk</a>' can be used to run AquaCompl,
including the necessary preparatory steps.</li>

<li>
Alternatively, the completeness check can be performed by the AQUA <a href="../server/.">server</a>.</li>

<li>
More documentation is available on the <a href="compl_method.html">methods</a>
of the program module AquaCompl.</li>
</ul>

<hr>
<p>Contact the <a href="mailto:jurgenfd@gmail.com">author</a> for help,
when required.
</body>
</html>
